The Remote Agent (RA) is an Artificial Intelligence (AI) system which automates some of the tasks normally reserved for human mission operators and performs these tasks autonomously on-board the spacecraft. These tasks include activity generation, sequencing, spacecraft analysis, and failure recovery. The RA will be demonstrated as a flight experiment on Deep Space One (DSI), the first deep space mission of the NASA's New Millennium Program (NMP). As we moved from prototyping into actual flight code development and teamed with ground operators, we made several major extensions to the RA architecture to address the broader operational context in which PA would be used. These extensions support ground operators and the RA sharing a long-range mission profile with facilities for asynchronous ground updates; support ground operators monitoring and commanding the spacecraft at multiple levels of detail simultaneously; and enable ground operators to provide additional knowledge to the RA, such as parameter updates, model updates, and diagnostic information, without interfering with the activities of the RA or leaving the system in an inconsistent state. The resulting architecture supports incremental autonomy, in which a basic agent can be delivered early and then used in an increasingly autonomous manner over the lifetime of the mission. It also supports variable autonomy, as it enables ground operators to benefit from autonomy when L'@ey want it, but does not inhibit them from obtaining a detailed understanding and exercising tighter control when necessary. These issues are critical to the successful development and operation of autonomous spacecraft.